Sandbox17



"'This sandbox is in use until August 1st, 2011 for Umass Chem 423 students. Others please do not edit this page. Thanks!'"

Lucia Tringali 3/31/11

Introduction
HIV protease is the essential catalytic enzyme that aids in the formation of mature functional HIV particles. Initially, HIV produces long polypeptide proteins. HIV protease is then essential to cleave these polypeptide proteins into smaller, functional proteins [1]. These smaller proteins then reassemble into replicable, mature, infectious HIV particles. HIV protease is a homodimer with the active site located at the dimer interface [2].

Darunavir is the most recent, second generation, protease inhibitor used to treat HIV. In June of 2006, Darunavir was FDA approved for use in combination with Ritonavir [3]. Also known as TMC 114, Darunavir binds directly to the binding site of HIV protease with higher affinity than previous protease inhibitors [4]. Studies have proven its effectiveness against both wild-type and resistant strains of HIV. It is administered as 375/50 to 600/100 Darunavir/Ritonavir mg tablets twice per day depending on the weight of the patient.

Overall Structure
Darunavir is oral second generation protease inhibitor. The drug has the chemical formula of C27H37N3O7S with a molecular weight of 547.6 g/mol. As a peptidomimetic HIV-1-protease inhibitor, it selectively inhibits the cleavage of HIV encoded Gag-Pol polyproteins.the drug, itself mainly binds to α-acid glycoprotein,20,21 and albumin. Darunavir contains both 3(R ),3a(S),6a(R)- bis-tetrahydrofuranylurethane (bis-THF) and a sulfonamide isostere. Two THF rings are fused together within the structure which provided 6 hydrogens strengthening the interaction of darunavir and HIV-1-protease Asp29 and Asp30 NHs. Bis-THF ligands also effectively fills in the hydrophobic pocket within the protein, allowing form maximized hydrogen bonding interactions with the backbone atoms of the S2-site. Darunavir conists of 99 amino acid monomers with a C2 axis of symmetry. It has 10 H bond acceptors and 4 H bond donors.there are a total of 2 alpha helices within the structure along with 14 beta sheets The overall structure is stabilized by hydrophobic burial of side changes and antiparallel interactions. Numerous backbone to backbone hydrogen bonds from with the substrate binding cleft. Darunavir also has the ability to alter to a conformation thereby fitting into the substrate envelope of HIV-1-protease's active site.

Drug Binding Site
The complex of HIV-1 Protease when bound to Darunavir prevents dimerization and typical catalytic activity of HIV-1 Protease; therefore, Darunavir is classified as an inhibitor. Binding to Darunavir also will inhibit cleavage of the HIV encoded GAG-POL polyproteins in virus-infected cells. This thus prevents the formation of mature infectious virus particles.

Darunavir binds to two distinct areas of the HIV protease protein. These sites are known as the active site shown as the orange sections, and at the surface of one of the flexible flaps in the protease dimer. The active site occurs at residues 25-27 (Asp-Thr-Gly) of the first beta strand and residues 125-127 (Asp-Thr-Gly) of the second beta chain. As you can see from the active site scene, these two different locations on two different beta strands are very close to one another. The two beta strands form a central cavity within the proteins core, where these two strands create an open active site. The drug Darunavir can easily bind to this cavity because it is readily available and all formed bonds will be identical.

Additional Features
Absorption, distribution, and metabolism. Orally co-administered Darunavir with low-dose ritonavir (100mg) (DRV/r) 600/100 mg twice daily is rapidly absorbed, reaching peak plasma concentrations within 2.5 to 4hours. Darunavir is metabolized by the hepatic cytochrome P450, in particualar CYP3A. Ritonavir acts as an inhibitor of CYP3A, therefore inhibiting the hepatic first class of Darunavir, an effect which is not enhanced with increase in ritonavir. Darunavir is mainly protein bound (95%) and although no change in total plasma, the concentration of unbound darunavir was increased in patients with mild or moderate liver disease.

Credits
Introduction - Jackie Somadelis

Overall Structure - shaina Boyle

Drug Binding Site - Lucia Tringali

Additional Features - Dany Mbakop